ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions
Open accessPublished version of a preprint
Abstract
SUMMARY: We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. AVAILABILITY AND IMPLEMENTATION: ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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- Authors
- Dolzhenko, E., Deshpande, V., Schlesinger, F., Krusche, P., Petrovski, R., Chen, S., Emig-Agius, D., Gross, A., Narzisi, G., Bowman, B., Scheffler, K., van Vugt, J. J. F. A., French, C., Sanchis-Juan, A., Ibáñez, K., Tucci, A., Lajoie, B. R., Veldink, J. H., Raymond, F. L., Taft, R. J., Bentley, D. R., & Eberle, M. A.
- Affiliations
- Illumina (United States) (US)
- Illumina (United Kingdom) (GB)
- New York Genome Center (US)
- UMC Utrecht Brain Center, Utrecht University , 3508 AB Utrecht, The Netherlands
- National Health Service (GB)
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre , Cambridge, CB2 0PT, UK
- Queen Mary University of London (GB)
- Utrecht University (NL)
- Corresponding author
- Eberle, Michael A
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-05-27
- Volume
- 35
- Issue
- 22
- Pages
- 4754-4756
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC6853681
- OpenAlex
- W2950733238
- Cited by
- 394
- References
- 20
- Citations by year
- 2026: 63 · 2025: 80 · 2024: 86 · 2023: 56 · 2022: 45 · 2021: 31 · 2020: 26 · 2019: 6 · 2012: 1
- FWCI
- 8.89
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion, cc-by-nc)
- Funders
- Universitätsklinikum Essen
- Medical Research Council (MR/S006753/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- microsatellite markers, sequence graphs, imperfect repeats, targeted genotyping, genetic variation
- MeSH terms
- Genotype, Software, Microsatellite Repeats
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